Dangers of modifying a manufacturer firmware

I have a device that uses UBIFS instead of YAFFS, and the system partition is truly read-only. As a result, I can only modify the system partition by completely reflashing it. My device is also not fastboot-friendly, so the only way I can flash it is to modify the manufacturer firmware. Naturally, I would like to root it this way. If I modify the manufacturer firmware, **test it in an avd**, and it **WORKS**, and then flash it to my device using stock recovery, what are the risks/chances that something will go wrong?